[gmx-users] (no subject)

[Justin A. Lemkul]

Sai Janani Ganesan wrote:
> Hi,
> 
> Thanks for the reply!
> 
> I tried the rates, and only the terminal with positive rate gets pulled.
> 
> The first and the last amino acids are spatially oriented one behind the 
> other. I think defining a vector might work better, but I am not sure 
> why nothing happens when I define a pull_vec1 and pull_vec2. Am I 
> missing anything?
> 

When setting "distance" as the pull_geometry, only pull_dim is used; pull_vec is 
ignored.  If you want to define vectors, use the "direction" pull_geometry.

-Justin

> Thanks,
> Sai
> 
> 
> 
> On Thu, Oct 6, 2011 at 9:14 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Sai Janani Ganesan wrote:
> 
>         Hi,
> 
>         I am trying to pull the first from the last amino acid of a
>         protein to completely unfold the protein in the X direction. I
>         chose the middle amino acid as the reference, and the groups get
>         pulled in the same direction or opposite direction (which is
>         what I want) depending on the trial. I am trying to find a
>         definite method to completely unfold it.
>         I define a different vector (pull_vec1 and pull_vec2) with +x
>         and -x values and that does not even pull the protein
>         I tried using only pull_group1 and pull_group2, without a
>         reference, and neither groups get pulled.
>         I chose different references, I do have some success but I don't
>         think it is the best way to do it.
> 
>         How do I pull the N and C terminal apart, by simultaneously
>         pulling them in opposite directions?Why is my vector definition
>         wrong?
> 
>         This is my pull code:
> 
>         pull            = umbrella
>         pull_geometry   = distance
>         pull_dim        = Y N N
>         pull_start      = yes      pull_ngroups    = 2
>         pull_group0     = Chain-C
>         pull_group1     = Chain-B
>         pull_group2     = Chain-A
> 
>         %pull_vec1      = -31 0 0
>         %pull_vec2      = 31 0 0
> 
> 
>     I suspect the % signs will mess things up, but probably will give a
>     fatal error, if nothing else.
> 
> 
>         pull_rate1      = 0.002    pull_k1         = 1000    pull_rate2
>              = 0.002     pull_k2         = 1000    
> 
> 
>     Here's the problem.  You're telling the two pulled groups to move in
>     the same direction.  With "distance" geometry, the selections are a
>     bit more simplistic.  If you set pull_rate1 to -0.002 and pull_rate2
>     to 0.002, the groups will be pulled in opposite directions.
>      Otherwise, you're just towing your protein along in the box.
> 
>     -Justin
> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>     ==============================__==========
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> 
> 
> -- 
> 
> /"Every sentence I utter must be understood not as an affirmation but as 
> a question." - Niels Bohr/

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================